Mantaflow simulation is baking the fluid in the wrong place and at the wrong scale
The fluid simulation is sensitive to the scale of the domain mesh - if it is has been rescaled (resized in any way) you should Apply Scale to ensure the scale is set back to 1.0 in each dimension. In your case, the adjusted scale (possible negative scale) was affecting the results of the simulation.
To address this, select the Domain object and press Ctrl+A and select Scale to 'Apply Scale' (the same option is availble through Object/Apply/Scale menu). You should then Free and re-Bake your simulation if necessary - to pick up the changes.